Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold447
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 18298
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:919 original size:7 final size:7
Alignment explanation
Indices: 907--936 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
897 CCATAGCCCT
907 TTTCATA
1 TTTCATA
914 TTTCATA
1 TTTCATA
921 TTTCATA
1 TTTCATA
928 TTTCATA
1 TTTCATA
935 TT
1 TT
937 ACTGGGCCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTCATA
Found at i:1199 original size:24 final size:24
Alignment explanation
Indices: 1161--1337 Score: 227
Period size: 24 Copynumber: 7.4 Consensus size: 24
1151 CTAGAGGCCT
*
1161 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
*
1186 AGCCCTTTTTATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
1210 AGCCCTTTATCATAACT-GGGCATA
1 AGCCCTTT-TAATAACTGGGGCATA
* *
1234 AGCCCTTCATCATAACTGGGGCATA
1 AGCCCTT-TTAATAACTGGGGCATA
*
1259 AGCCCTTTATCATAACTGGGGCATA
1 AGCCCTTT-TAATAACTGGGGCATA
*
1284 AGCCC-TTTAATAATTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
1307 AGCCC-TTTAATAACT-GGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
1329 AGCCCTTTT
1 AGCCCTTTT
1338 GCACTTCCTC
Statistics
Matches: 139, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
22 12 0.09
23 31 0.22
24 50 0.36
25 46 0.33
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:1199 original size:49 final size:48
Alignment explanation
Indices: 1161--1337 Score: 227
Period size: 49 Copynumber: 3.7 Consensus size: 48
1151 CTAGAGGCCT
*
1161 AGCCTCTTT-TAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATA
1 AGCC-CTTTATAATAACT-GGGCATAAGCCCTTTTTATAACTGGGGCATA
* * *
1210 AGCCCTTTATCATAACTGGGCATAAGCCCTTCATCATAACTGGGGCATA
1 AGCCCTTTATAATAACTGGGCATAAGCCCTT-TTTATAACTGGGGCATA
* * *
1259 AGCCCTTTATCATAACTGGGGCATAAGCCC-TTTAATAATTGGGGCATA
1 AGCCCTTTATAATAACT-GGGCATAAGCCCTTTTTATAACTGGGGCATA
1307 AGCCC-TT-TAATAACTGGGCATAAGCCCTTTT
1 AGCCCTTTATAATAACTGGGCATAAGCCCTTTT
1338 GCACTTCCTC
Statistics
Matches: 116, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
45 12 0.10
46 10 0.09
47 2 0.02
48 36 0.31
49 44 0.38
50 12 0.10
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (48 bp):
AGCCCTTTATAATAACTGGGCATAAGCCCTTTTTATAACTGGGGCATA
Found at i:1409 original size:9 final size:9
Alignment explanation
Indices: 1395--1451 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
1385 ATCTCATGTG
1395 CATATCATA
1 CATATCATA
*
1404 CATATCATGTG
1 CATATCA--TA
1415 CATATCATA
1 CATATCATA
* *
1424 CATGTCATGTG
1 CATATCA--TA
1435 CATATCATA
1 CATATCATA
1444 CATATCAT
1 CATATCAT
1452 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:1411 original size:20 final size:20
Alignment explanation
Indices: 1383--1453 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
1373 GCATTTATGA
*
1383 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
1403 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
1423 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
1443 ACATATCATGT
1 ACATATCATGT
1454 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:1418 original size:11 final size:11
Alignment explanation
Indices: 1388--1442 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
1378 TATGAACATC
1388 TCATGTGCATA
1 TCATGTGCATA
*
1399 TCA--TACATA
1 TCATGTGCATA
1408 TCATGTGCATA
1 TCATGTGCATA
* *
1419 TCA--TACATG
1 TCATGTGCATA
1428 TCATGTGCATA
1 TCATGTGCATA
1439 TCAT
1 TCAT
1443 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:2755 original size:27 final size:27
Alignment explanation
Indices: 2693--2770 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
2683 GGGCATATTC
2693 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
2720 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
* *
2747 GTCTTTTTACC-TAATAGGGGTATT
1 GTCATTTTACCAT-ACAGGGGTATT
2771 TTAGTCATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.05
27 40 0.93
28 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:2841 original size:27 final size:27
Alignment explanation
Indices: 2808--3093 Score: 195
Period size: 27 Copynumber: 10.6 Consensus size: 27
2798 TTGGTAAATC
*
2808 TACAAACCAAGGGTATTTCAGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
** * *
2835 TGTAAACCAATGGTATTTCTA-TAATTTT
1 TACAAATCAAGGGTATTTC-AGTAA-TTT
* * *
2863 TAGAAAGTCAAGGGTATTTCTGTAACTT
1 TACAAA-TCAAGGGTATTTCAGTAATTT
** * **
2891 TGTAAATCAGGGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
** *
2918 TACAAATTGAGGGTATTTCGGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* * **
2945 CACAAA-CCAGTGGTATTTTGGTAATTT
1 TACAAATCAAG-GGTATTTCAGTAATTT
* **
2972 TACAAA-CTAGGGGTATTTTGGTAATTT
1 TACAAATC-AAGGGTATTTCAGTAATTT
** *
2999 TACAAATTGAGGGTATTTCTGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* *
3026 TACAAACCAAGGGTATTTTAGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* *
3053 TACAGA-CTAGGGTA-TTCTAGTAATTT
1 TACAAATCAAGGGTATTTC-AGTAATTT
**
3079 TGTAAATCAAGGGTA
1 TACAAATCAAGGGTA
3094 AAATAGTAAT
Statistics
Matches: 205, Mismatches: 45, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
25 2 0.01
26 20 0.10
27 154 0.75
28 15 0.07
29 14 0.07
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
TACAAATCAAGGGTATTTCAGTAATTT
Found at i:2994 original size:81 final size:81
Alignment explanation
Indices: 2899--3079 Score: 285
Period size: 81 Copynumber: 2.2 Consensus size: 81
2889 TTTGTAAATC
2899 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACC-AGTGGTATTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAG-GGTATTT
*
2963 TGGTAATTTTACAAACT
65 TAGTAATTTTACAAACT
* *
2980 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCTGTAATTTTACAAACCAAGGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTT
*
3045 AGTAATTTTACAGACT
66 AGTAATTTTACAAACT
* *
3061 A-GGGTATTCTAGTAATTTT
1 AGGGGTATTTTGGTAATTTT
3080 GTAAATCAAG
Statistics
Matches: 93, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
80 16 0.17
81 75 0.81
82 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTT
AGTAATTTTACAAACT
Found at i:3198 original size:27 final size:27
Alignment explanation
Indices: 3071--3191 Score: 152
Period size: 27 Copynumber: 4.5 Consensus size: 27
3061 AGGGTATTCT
* *
3071 AGTAATTTTGTAAATCAAGGGTAAAAT
1 AGTAATTCTGTAAATCAAGGGTAAAAC
3098 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* *
3125 AGTAATTCTATAAATCAAGGATAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* * * * *
3152 GGTACTTTTATAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
*
3179 GGTAATTCTGTAA
1 AGTAATTCTGTAA
3192 GTCGAGGTAA
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (27 bp):
AGTAATTCTGTAAATCAAGGGTAAAAC
Found at i:3292 original size:27 final size:27
Alignment explanation
Indices: 3234--3310 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
3224 TGTAAATCGG
* * *
3234 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTACTTTAGTAATTTTACAAATCCA
*
3261 AGGTACTTTAGTAATTTTACAAATCCA
1 GGGTACTTTAGTAATTTTACAAATCCA
*
3288 GGGTA-TTTCAGTATTTTTACAAA
1 GGGTACTTT-AGTAATTTTACAAA
3311 CTAAGCGTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 3 0.07
27 40 0.93
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (27 bp):
GGGTACTTTAGTAATTTTACAAATCCA
Found at i:3340 original size:28 final size:27
Alignment explanation
Indices: 3244--3342 Score: 78
Period size: 27 Copynumber: 3.6 Consensus size: 27
3234 GGGTACTTTG
* *
3244 GTAATTTTACAAGTCGAAG-GTACTTT-A
1 GTAATTTTACAA-ACTAAGCGTA-TTTCA
* *
3271 GTAATTTTACAAA-TCCAGGGTATTTCA
1 GTAATTTTACAAACT-AAGCGTATTTCA
* *
3298 GTATTTTTACAAACTAAGCGTATTTCG
1 GTAATTTTACAAACTAAGCGTATTTCA
*
3325 GTAATTTTAGTAAACTAA
1 GTAATTTTA-CAAACTAA
3343 AGTATTTTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
26 5 0.09
27 45 0.78
28 8 0.14
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGCGTATTTCA
Found at i:5600 original size:40 final size:40
Alignment explanation
Indices: 5516--5739 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
5506 TTGAATGATG
* * * *
5516 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
5556 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
5596 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
5634 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
5674 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
5715 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
5740 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 25 0.15
39 19 0.12
40 111 0.67
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:5734 original size:80 final size:80
Alignment explanation
Indices: 5516--5739 Score: 296
Period size: 78 Copynumber: 2.8 Consensus size: 80
5506 TTGAATGATG
* * * * *
5516 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
5579 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
*
5596 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
5658 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* *
5674 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
5739 G
66 G
5740 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
77 2 0.02
78 49 0.39
79 25 0.20
80 49 0.39
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:13592 original size:40 final size:40
Alignment explanation
Indices: 13508--13731 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
13498 TTGAATGATG
* * * *
13508 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
13548 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
13588 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
13626 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
13666 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
13707 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
13732 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 25 0.15
39 19 0.12
40 111 0.67
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:13726 original size:80 final size:80
Alignment explanation
Indices: 13508--13731 Score: 296
Period size: 78 Copynumber: 2.8 Consensus size: 80
13498 TTGAATGATG
* * * * *
13508 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
13571 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
*
13588 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
13650 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* *
13666 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
13731 G
66 G
13732 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
77 2 0.02
78 49 0.39
79 25 0.20
80 49 0.39
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Done.